Multiple sequence alignment - TraesCS4A01G219800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G219800 chr4A 100.000 3351 0 0 1 3351 521944567 521947917 0.000000e+00 6189.0
1 TraesCS4A01G219800 chr4A 77.600 125 27 1 280 403 703940410 703940534 1.290000e-09 75.0
2 TraesCS4A01G219800 chr2A 94.925 2601 114 11 605 3197 461392275 461394865 0.000000e+00 4056.0
3 TraesCS4A01G219800 chr3A 94.753 2592 121 10 612 3197 37632900 37635482 0.000000e+00 4019.0
4 TraesCS4A01G219800 chr3A 93.693 2616 129 15 610 3199 715213481 715216086 0.000000e+00 3884.0
5 TraesCS4A01G219800 chr3A 93.254 2609 127 15 611 3199 27908721 27906142 0.000000e+00 3797.0
6 TraesCS4A01G219800 chr1A 94.203 2605 126 13 612 3199 302911829 302914425 0.000000e+00 3951.0
7 TraesCS4A01G219800 chr7A 93.435 2696 117 24 607 3275 147920466 147917804 0.000000e+00 3943.0
8 TraesCS4A01G219800 chr7A 79.339 121 16 7 283 403 63731689 63731800 3.590000e-10 76.8
9 TraesCS4A01G219800 chr4B 92.127 2769 162 27 612 3351 657805506 657802765 0.000000e+00 3855.0
10 TraesCS4A01G219800 chr4B 87.705 610 68 4 2 611 103227042 103227644 0.000000e+00 704.0
11 TraesCS4A01G219800 chr4B 95.455 44 2 0 340 383 538708651 538708608 1.670000e-08 71.3
12 TraesCS4A01G219800 chr4B 100.000 28 0 0 430 457 103227570 103227597 6.000000e-03 52.8
13 TraesCS4A01G219800 chr3D 91.317 2787 153 33 610 3351 20288616 20291358 0.000000e+00 3723.0
14 TraesCS4A01G219800 chr3D 91.200 2784 157 32 612 3351 523400411 523403150 0.000000e+00 3703.0
15 TraesCS4A01G219800 chr3D 93.958 1473 48 11 1906 3351 160918205 160919663 0.000000e+00 2189.0
16 TraesCS4A01G219800 chr3D 75.132 378 75 15 77 445 374037546 374037179 3.460000e-35 159.0
17 TraesCS4A01G219800 chr1D 91.325 2778 150 38 611 3351 30073892 30071169 0.000000e+00 3711.0
18 TraesCS4A01G219800 chr1D 73.359 259 54 11 207 462 460981176 460980930 7.710000e-12 82.4
19 TraesCS4A01G219800 chr6D 89.964 2760 172 57 611 3351 175423682 175426355 0.000000e+00 3465.0
20 TraesCS4A01G219800 chr5A 96.376 1959 70 1 611 2569 647551124 647553081 0.000000e+00 3223.0
21 TraesCS4A01G219800 chr5A 95.202 1980 86 6 612 2585 680753169 680755145 0.000000e+00 3121.0
22 TraesCS4A01G219800 chr5A 91.892 814 37 9 2540 3351 647552996 647553782 0.000000e+00 1110.0
23 TraesCS4A01G219800 chr6A 94.978 2011 86 9 611 2606 428285584 428287594 0.000000e+00 3140.0
24 TraesCS4A01G219800 chr6A 94.557 1874 80 13 1339 3197 608061677 608063543 0.000000e+00 2876.0
25 TraesCS4A01G219800 chr5D 94.044 1746 59 15 1636 3351 494244468 494242738 0.000000e+00 2606.0
26 TraesCS4A01G219800 chr4D 87.582 612 49 8 5 611 69737943 69738532 0.000000e+00 684.0
27 TraesCS4A01G219800 chr6B 74.900 251 60 2 231 478 208029843 208029593 9.830000e-21 111.0
28 TraesCS4A01G219800 chr1B 72.598 281 67 8 104 383 632036747 632037018 2.140000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G219800 chr4A 521944567 521947917 3350 False 6189.0 6189 100.0000 1 3351 1 chr4A.!!$F1 3350
1 TraesCS4A01G219800 chr2A 461392275 461394865 2590 False 4056.0 4056 94.9250 605 3197 1 chr2A.!!$F1 2592
2 TraesCS4A01G219800 chr3A 37632900 37635482 2582 False 4019.0 4019 94.7530 612 3197 1 chr3A.!!$F1 2585
3 TraesCS4A01G219800 chr3A 715213481 715216086 2605 False 3884.0 3884 93.6930 610 3199 1 chr3A.!!$F2 2589
4 TraesCS4A01G219800 chr3A 27906142 27908721 2579 True 3797.0 3797 93.2540 611 3199 1 chr3A.!!$R1 2588
5 TraesCS4A01G219800 chr1A 302911829 302914425 2596 False 3951.0 3951 94.2030 612 3199 1 chr1A.!!$F1 2587
6 TraesCS4A01G219800 chr7A 147917804 147920466 2662 True 3943.0 3943 93.4350 607 3275 1 chr7A.!!$R1 2668
7 TraesCS4A01G219800 chr4B 657802765 657805506 2741 True 3855.0 3855 92.1270 612 3351 1 chr4B.!!$R2 2739
8 TraesCS4A01G219800 chr4B 103227042 103227644 602 False 378.4 704 93.8525 2 611 2 chr4B.!!$F1 609
9 TraesCS4A01G219800 chr3D 20288616 20291358 2742 False 3723.0 3723 91.3170 610 3351 1 chr3D.!!$F1 2741
10 TraesCS4A01G219800 chr3D 523400411 523403150 2739 False 3703.0 3703 91.2000 612 3351 1 chr3D.!!$F3 2739
11 TraesCS4A01G219800 chr3D 160918205 160919663 1458 False 2189.0 2189 93.9580 1906 3351 1 chr3D.!!$F2 1445
12 TraesCS4A01G219800 chr1D 30071169 30073892 2723 True 3711.0 3711 91.3250 611 3351 1 chr1D.!!$R1 2740
13 TraesCS4A01G219800 chr6D 175423682 175426355 2673 False 3465.0 3465 89.9640 611 3351 1 chr6D.!!$F1 2740
14 TraesCS4A01G219800 chr5A 680753169 680755145 1976 False 3121.0 3121 95.2020 612 2585 1 chr5A.!!$F1 1973
15 TraesCS4A01G219800 chr5A 647551124 647553782 2658 False 2166.5 3223 94.1340 611 3351 2 chr5A.!!$F2 2740
16 TraesCS4A01G219800 chr6A 428285584 428287594 2010 False 3140.0 3140 94.9780 611 2606 1 chr6A.!!$F1 1995
17 TraesCS4A01G219800 chr6A 608061677 608063543 1866 False 2876.0 2876 94.5570 1339 3197 1 chr6A.!!$F2 1858
18 TraesCS4A01G219800 chr5D 494242738 494244468 1730 True 2606.0 2606 94.0440 1636 3351 1 chr5D.!!$R1 1715
19 TraesCS4A01G219800 chr4D 69737943 69738532 589 False 684.0 684 87.5820 5 611 1 chr4D.!!$F1 606

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
90 91 0.030705 TATCCTCCCCTCTGCTTGCT 60.031 55.0 0.0 0.0 0.00 3.91 F
547 552 0.034896 ATTGTTCCGCACGAGGACTT 59.965 50.0 0.0 0.0 40.56 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1468 1555 5.357032 CCATAGAAACGCCTTCCTGTTAAAT 59.643 40.0 0.0 0.0 34.21 1.40 R
2449 2566 6.597562 ACACTAGGTTAAACTTCACATTCCA 58.402 36.0 0.0 0.0 0.00 3.53 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.179045 CTCCCCCTCATGTTAAGGCG 60.179 60.000 0.00 0.00 32.15 5.52
26 27 1.412710 CTCATGTTAAGGCGGCTAGGA 59.587 52.381 13.71 2.29 0.00 2.94
86 87 1.224120 TGGATTATCCTCCCCTCTGCT 59.776 52.381 12.91 0.00 37.46 4.24
90 91 0.030705 TATCCTCCCCTCTGCTTGCT 60.031 55.000 0.00 0.00 0.00 3.91
121 122 2.124695 GTGGCGGTGAGGGGAATC 60.125 66.667 0.00 0.00 0.00 2.52
132 133 2.190578 GGGAATCCCTGTGCCTCG 59.809 66.667 11.95 0.00 41.34 4.63
136 137 2.543067 GAATCCCTGTGCCTCGGCTT 62.543 60.000 9.65 0.00 42.51 4.35
158 159 7.069702 GGCTTGGACTAGTAGTTTAGGTTAGAT 59.930 40.741 3.85 0.00 0.00 1.98
178 179 1.770061 TGTTTTTAGTCCTCACGGGGT 59.230 47.619 0.00 0.00 35.33 4.95
190 191 4.351938 CGGGGTGACGCTTCGACA 62.352 66.667 0.00 0.00 42.01 4.35
195 196 1.007734 GTGACGCTTCGACAGGTGA 60.008 57.895 0.00 0.00 32.07 4.02
213 214 1.369091 GACGGCGCACCATCTTTGAT 61.369 55.000 10.83 0.00 34.57 2.57
224 225 4.523943 CACCATCTTTGATTTGGTCTTCCA 59.476 41.667 0.00 0.00 41.77 3.53
240 241 1.573108 TCCAAGCTTCGATTCTCCCT 58.427 50.000 0.00 0.00 0.00 4.20
245 246 2.183679 AGCTTCGATTCTCCCTGAGTT 58.816 47.619 0.00 0.00 0.00 3.01
251 252 1.825474 GATTCTCCCTGAGTTCGTCCA 59.175 52.381 0.00 0.00 0.00 4.02
253 254 1.938585 TCTCCCTGAGTTCGTCCATT 58.061 50.000 0.00 0.00 0.00 3.16
292 293 4.582869 AGCTGCAACATAGATTCTTGTCA 58.417 39.130 1.02 0.00 0.00 3.58
327 328 2.022195 CGAGGTTAGGGATTCTCGTCA 58.978 52.381 0.00 0.00 42.61 4.35
361 366 0.798776 CGAGATTTGGTGTCAGGTGC 59.201 55.000 0.00 0.00 0.00 5.01
379 384 3.499918 GGTGCTTCATATCGATTCAAGGG 59.500 47.826 1.71 0.00 0.00 3.95
380 385 4.130118 GTGCTTCATATCGATTCAAGGGT 58.870 43.478 1.71 0.00 0.00 4.34
381 386 4.576463 GTGCTTCATATCGATTCAAGGGTT 59.424 41.667 1.71 0.00 0.00 4.11
382 387 4.816385 TGCTTCATATCGATTCAAGGGTTC 59.184 41.667 1.71 0.00 0.00 3.62
383 388 4.084328 GCTTCATATCGATTCAAGGGTTCG 60.084 45.833 1.71 0.00 0.00 3.95
384 389 4.929819 TCATATCGATTCAAGGGTTCGA 57.070 40.909 1.71 0.00 44.93 3.71
385 390 4.871513 TCATATCGATTCAAGGGTTCGAG 58.128 43.478 1.71 0.00 44.17 4.04
386 391 2.604046 ATCGATTCAAGGGTTCGAGG 57.396 50.000 0.00 0.00 44.17 4.63
387 392 1.552578 TCGATTCAAGGGTTCGAGGA 58.447 50.000 0.00 0.00 37.01 3.71
388 393 2.108168 TCGATTCAAGGGTTCGAGGAT 58.892 47.619 0.00 0.00 37.01 3.24
389 394 2.159099 TCGATTCAAGGGTTCGAGGATG 60.159 50.000 0.00 0.00 37.01 3.51
390 395 2.159099 CGATTCAAGGGTTCGAGGATGA 60.159 50.000 0.00 0.00 34.92 2.92
391 396 2.762535 TTCAAGGGTTCGAGGATGAC 57.237 50.000 0.00 0.00 0.00 3.06
392 397 0.530744 TCAAGGGTTCGAGGATGACG 59.469 55.000 0.00 0.00 0.00 4.35
393 398 0.530744 CAAGGGTTCGAGGATGACGA 59.469 55.000 0.00 0.00 37.99 4.20
394 399 0.531200 AAGGGTTCGAGGATGACGAC 59.469 55.000 0.00 0.00 39.46 4.34
395 400 0.323542 AGGGTTCGAGGATGACGACT 60.324 55.000 0.00 0.00 39.46 4.18
396 401 1.064906 AGGGTTCGAGGATGACGACTA 60.065 52.381 0.00 0.00 39.46 2.59
397 402 1.065251 GGGTTCGAGGATGACGACTAC 59.935 57.143 0.00 0.00 39.46 2.73
398 403 1.267932 GGTTCGAGGATGACGACTACG 60.268 57.143 0.00 0.00 45.75 3.51
399 404 1.012086 TTCGAGGATGACGACTACGG 58.988 55.000 0.00 0.00 44.46 4.02
406 411 3.900855 GACGACTACGGCTCCAGA 58.099 61.111 0.00 0.00 45.04 3.86
407 412 1.428620 GACGACTACGGCTCCAGAC 59.571 63.158 0.00 0.00 45.04 3.51
408 413 1.002379 ACGACTACGGCTCCAGACT 60.002 57.895 0.00 0.00 44.46 3.24
409 414 1.306642 ACGACTACGGCTCCAGACTG 61.307 60.000 0.00 0.00 44.46 3.51
410 415 1.139947 GACTACGGCTCCAGACTGC 59.860 63.158 0.00 0.00 0.00 4.40
411 416 1.304547 ACTACGGCTCCAGACTGCT 60.305 57.895 0.00 0.00 0.00 4.24
412 417 1.140589 CTACGGCTCCAGACTGCTG 59.859 63.158 0.00 0.00 41.93 4.41
422 427 0.539051 CAGACTGCTGGTCCTTAGGG 59.461 60.000 0.00 0.00 45.54 3.53
423 428 0.618968 AGACTGCTGGTCCTTAGGGG 60.619 60.000 0.00 0.00 45.54 4.79
424 429 2.258748 GACTGCTGGTCCTTAGGGGC 62.259 65.000 0.00 0.00 38.93 5.80
425 430 3.391665 CTGCTGGTCCTTAGGGGCG 62.392 68.421 0.00 0.00 38.30 6.13
426 431 4.858680 GCTGGTCCTTAGGGGCGC 62.859 72.222 0.00 0.00 38.30 6.53
427 432 4.530857 CTGGTCCTTAGGGGCGCG 62.531 72.222 0.00 0.00 38.30 6.86
429 434 4.832608 GGTCCTTAGGGGCGCGTG 62.833 72.222 8.43 0.00 38.30 5.34
432 437 4.856801 CCTTAGGGGCGCGTGCAT 62.857 66.667 24.18 10.49 45.35 3.96
433 438 3.576356 CTTAGGGGCGCGTGCATG 61.576 66.667 24.18 0.09 45.35 4.06
434 439 4.089239 TTAGGGGCGCGTGCATGA 62.089 61.111 24.18 1.67 45.35 3.07
435 440 4.529219 TAGGGGCGCGTGCATGAG 62.529 66.667 24.18 7.88 45.35 2.90
440 445 3.121030 GCGCGTGCATGAGGACTT 61.121 61.111 17.66 0.00 42.15 3.01
441 446 3.084579 CGCGTGCATGAGGACTTC 58.915 61.111 10.93 0.00 33.37 3.01
442 447 1.737735 CGCGTGCATGAGGACTTCA 60.738 57.895 10.93 0.00 40.85 3.02
454 459 5.955961 TGAGGACTTCATGGTTATCATCA 57.044 39.130 0.00 0.00 32.92 3.07
455 460 5.922053 TGAGGACTTCATGGTTATCATCAG 58.078 41.667 0.00 0.00 32.92 2.90
456 461 4.712476 AGGACTTCATGGTTATCATCAGC 58.288 43.478 0.00 0.00 32.92 4.26
457 462 4.164796 AGGACTTCATGGTTATCATCAGCA 59.835 41.667 0.00 0.00 32.92 4.41
458 463 4.883585 GGACTTCATGGTTATCATCAGCAA 59.116 41.667 0.00 0.00 32.92 3.91
459 464 5.008415 GGACTTCATGGTTATCATCAGCAAG 59.992 44.000 0.00 0.00 32.92 4.01
460 465 4.885907 ACTTCATGGTTATCATCAGCAAGG 59.114 41.667 0.00 0.00 32.92 3.61
461 466 4.508551 TCATGGTTATCATCAGCAAGGT 57.491 40.909 0.00 0.00 32.92 3.50
462 467 4.858850 TCATGGTTATCATCAGCAAGGTT 58.141 39.130 0.00 0.00 32.92 3.50
463 468 6.000246 TCATGGTTATCATCAGCAAGGTTA 58.000 37.500 0.00 0.00 32.92 2.85
464 469 6.057533 TCATGGTTATCATCAGCAAGGTTAG 58.942 40.000 0.00 0.00 32.92 2.34
465 470 4.780815 TGGTTATCATCAGCAAGGTTAGG 58.219 43.478 0.00 0.00 0.00 2.69
466 471 4.227300 TGGTTATCATCAGCAAGGTTAGGT 59.773 41.667 0.00 0.00 0.00 3.08
467 472 4.816925 GGTTATCATCAGCAAGGTTAGGTC 59.183 45.833 0.00 0.00 0.00 3.85
468 473 2.672961 TCATCAGCAAGGTTAGGTCG 57.327 50.000 0.00 0.00 0.00 4.79
469 474 1.207089 TCATCAGCAAGGTTAGGTCGG 59.793 52.381 0.00 0.00 0.00 4.79
470 475 0.107654 ATCAGCAAGGTTAGGTCGGC 60.108 55.000 0.00 0.00 0.00 5.54
471 476 1.192146 TCAGCAAGGTTAGGTCGGCT 61.192 55.000 0.00 0.00 0.00 5.52
472 477 0.741221 CAGCAAGGTTAGGTCGGCTC 60.741 60.000 0.00 0.00 0.00 4.70
473 478 1.449778 GCAAGGTTAGGTCGGCTCC 60.450 63.158 0.00 0.00 0.00 4.70
474 479 1.980052 CAAGGTTAGGTCGGCTCCA 59.020 57.895 0.00 0.00 0.00 3.86
475 480 0.108138 CAAGGTTAGGTCGGCTCCAG 60.108 60.000 0.00 0.00 0.00 3.86
476 481 0.544595 AAGGTTAGGTCGGCTCCAGT 60.545 55.000 0.00 0.00 0.00 4.00
477 482 0.333993 AGGTTAGGTCGGCTCCAGTA 59.666 55.000 0.00 0.00 0.00 2.74
478 483 1.063114 AGGTTAGGTCGGCTCCAGTAT 60.063 52.381 0.00 0.00 0.00 2.12
479 484 1.068741 GGTTAGGTCGGCTCCAGTATG 59.931 57.143 0.00 0.00 0.00 2.39
480 485 2.029623 GTTAGGTCGGCTCCAGTATGA 58.970 52.381 0.00 0.00 39.69 2.15
481 486 2.429610 GTTAGGTCGGCTCCAGTATGAA 59.570 50.000 0.00 0.00 39.69 2.57
482 487 1.568504 AGGTCGGCTCCAGTATGAAA 58.431 50.000 0.00 0.00 39.69 2.69
483 488 1.906574 AGGTCGGCTCCAGTATGAAAA 59.093 47.619 0.00 0.00 39.69 2.29
484 489 2.007608 GGTCGGCTCCAGTATGAAAAC 58.992 52.381 0.00 0.00 39.69 2.43
485 490 1.659098 GTCGGCTCCAGTATGAAAACG 59.341 52.381 0.00 0.00 39.69 3.60
486 491 1.006832 CGGCTCCAGTATGAAAACGG 58.993 55.000 0.00 0.00 39.69 4.44
487 492 0.733150 GGCTCCAGTATGAAAACGGC 59.267 55.000 0.00 0.00 39.69 5.68
488 493 0.373716 GCTCCAGTATGAAAACGGCG 59.626 55.000 4.80 4.80 39.69 6.46
489 494 2.004583 CTCCAGTATGAAAACGGCGA 57.995 50.000 16.62 0.00 39.69 5.54
490 495 1.659098 CTCCAGTATGAAAACGGCGAC 59.341 52.381 16.62 0.00 39.69 5.19
491 496 1.001068 TCCAGTATGAAAACGGCGACA 59.999 47.619 16.62 8.60 39.69 4.35
492 497 1.801771 CCAGTATGAAAACGGCGACAA 59.198 47.619 16.62 0.00 39.69 3.18
493 498 2.412325 CCAGTATGAAAACGGCGACAAC 60.412 50.000 16.62 2.76 39.69 3.32
494 499 2.222213 CAGTATGAAAACGGCGACAACA 59.778 45.455 16.62 8.98 39.69 3.33
495 500 2.873472 AGTATGAAAACGGCGACAACAA 59.127 40.909 16.62 0.00 0.00 2.83
496 501 2.113910 ATGAAAACGGCGACAACAAC 57.886 45.000 16.62 0.00 0.00 3.32
497 502 0.803117 TGAAAACGGCGACAACAACA 59.197 45.000 16.62 1.24 0.00 3.33
498 503 1.185189 GAAAACGGCGACAACAACAC 58.815 50.000 16.62 0.00 0.00 3.32
499 504 0.806241 AAAACGGCGACAACAACACT 59.194 45.000 16.62 0.00 0.00 3.55
500 505 0.375803 AAACGGCGACAACAACACTC 59.624 50.000 16.62 0.00 0.00 3.51
501 506 0.461339 AACGGCGACAACAACACTCT 60.461 50.000 16.62 0.00 0.00 3.24
502 507 0.386476 ACGGCGACAACAACACTCTA 59.614 50.000 16.62 0.00 0.00 2.43
503 508 1.000506 ACGGCGACAACAACACTCTAT 59.999 47.619 16.62 0.00 0.00 1.98
504 509 1.654105 CGGCGACAACAACACTCTATC 59.346 52.381 0.00 0.00 0.00 2.08
505 510 2.000447 GGCGACAACAACACTCTATCC 59.000 52.381 0.00 0.00 0.00 2.59
506 511 1.654105 GCGACAACAACACTCTATCCG 59.346 52.381 0.00 0.00 0.00 4.18
507 512 1.654105 CGACAACAACACTCTATCCGC 59.346 52.381 0.00 0.00 0.00 5.54
508 513 2.671351 CGACAACAACACTCTATCCGCT 60.671 50.000 0.00 0.00 0.00 5.52
509 514 3.427098 CGACAACAACACTCTATCCGCTA 60.427 47.826 0.00 0.00 0.00 4.26
510 515 4.106197 GACAACAACACTCTATCCGCTAG 58.894 47.826 0.00 0.00 0.00 3.42
511 516 3.510360 ACAACAACACTCTATCCGCTAGT 59.490 43.478 0.00 0.00 0.00 2.57
512 517 4.021368 ACAACAACACTCTATCCGCTAGTT 60.021 41.667 0.00 0.00 0.00 2.24
513 518 4.803098 ACAACACTCTATCCGCTAGTTT 57.197 40.909 0.00 0.00 0.00 2.66
514 519 5.148651 ACAACACTCTATCCGCTAGTTTT 57.851 39.130 0.00 0.00 0.00 2.43
515 520 4.929808 ACAACACTCTATCCGCTAGTTTTG 59.070 41.667 0.00 0.00 37.10 2.44
516 521 3.522553 ACACTCTATCCGCTAGTTTTGC 58.477 45.455 0.00 0.00 0.00 3.68
517 522 2.866762 CACTCTATCCGCTAGTTTTGCC 59.133 50.000 0.00 0.00 0.00 4.52
518 523 2.128035 CTCTATCCGCTAGTTTTGCCG 58.872 52.381 0.00 0.00 0.00 5.69
519 524 1.202486 TCTATCCGCTAGTTTTGCCGG 60.202 52.381 0.00 0.00 0.00 6.13
520 525 0.812412 TATCCGCTAGTTTTGCCGGC 60.812 55.000 22.73 22.73 0.00 6.13
521 526 4.160635 CCGCTAGTTTTGCCGGCG 62.161 66.667 23.90 6.39 44.48 6.46
522 527 4.160635 CGCTAGTTTTGCCGGCGG 62.161 66.667 24.35 24.35 41.77 6.13
523 528 3.053896 GCTAGTTTTGCCGGCGGT 61.054 61.111 28.82 8.95 0.00 5.68
524 529 1.742510 GCTAGTTTTGCCGGCGGTA 60.743 57.895 28.82 22.20 0.00 4.02
525 530 1.702491 GCTAGTTTTGCCGGCGGTAG 61.702 60.000 28.82 19.83 0.00 3.18
526 531 0.390735 CTAGTTTTGCCGGCGGTAGT 60.391 55.000 28.82 14.04 0.00 2.73
527 532 0.671163 TAGTTTTGCCGGCGGTAGTG 60.671 55.000 28.82 0.97 0.00 2.74
528 533 1.962306 GTTTTGCCGGCGGTAGTGA 60.962 57.895 28.82 10.22 0.00 3.41
529 534 1.003112 TTTTGCCGGCGGTAGTGAT 60.003 52.632 28.82 0.00 0.00 3.06
530 535 0.606944 TTTTGCCGGCGGTAGTGATT 60.607 50.000 28.82 0.00 0.00 2.57
531 536 1.302383 TTTGCCGGCGGTAGTGATTG 61.302 55.000 28.82 0.00 0.00 2.67
532 537 2.125269 GCCGGCGGTAGTGATTGT 60.125 61.111 28.82 0.00 0.00 2.71
533 538 1.743995 GCCGGCGGTAGTGATTGTT 60.744 57.895 28.82 0.00 0.00 2.83
534 539 1.702491 GCCGGCGGTAGTGATTGTTC 61.702 60.000 28.82 1.40 0.00 3.18
535 540 1.087771 CCGGCGGTAGTGATTGTTCC 61.088 60.000 19.97 0.00 0.00 3.62
536 541 1.418342 CGGCGGTAGTGATTGTTCCG 61.418 60.000 0.00 0.00 43.37 4.30
538 543 3.131326 CGGTAGTGATTGTTCCGCA 57.869 52.632 0.00 0.00 35.01 5.69
539 544 0.719465 CGGTAGTGATTGTTCCGCAC 59.281 55.000 0.00 0.00 35.01 5.34
540 545 0.719465 GGTAGTGATTGTTCCGCACG 59.281 55.000 0.00 0.00 37.60 5.34
541 546 1.670674 GGTAGTGATTGTTCCGCACGA 60.671 52.381 0.00 0.00 37.60 4.35
542 547 1.654105 GTAGTGATTGTTCCGCACGAG 59.346 52.381 0.00 0.00 37.60 4.18
543 548 0.670546 AGTGATTGTTCCGCACGAGG 60.671 55.000 0.00 0.00 37.60 4.63
544 549 0.669318 GTGATTGTTCCGCACGAGGA 60.669 55.000 0.00 0.00 38.79 3.71
545 550 0.669318 TGATTGTTCCGCACGAGGAC 60.669 55.000 0.00 0.00 40.56 3.85
546 551 0.389948 GATTGTTCCGCACGAGGACT 60.390 55.000 0.00 0.00 40.56 3.85
547 552 0.034896 ATTGTTCCGCACGAGGACTT 59.965 50.000 0.00 0.00 40.56 3.01
548 553 0.599204 TTGTTCCGCACGAGGACTTC 60.599 55.000 0.00 0.00 40.56 3.01
549 554 1.006571 GTTCCGCACGAGGACTTCA 60.007 57.895 0.00 0.00 40.56 3.02
550 555 0.389948 GTTCCGCACGAGGACTTCAT 60.390 55.000 0.00 0.00 40.56 2.57
551 556 0.389817 TTCCGCACGAGGACTTCATG 60.390 55.000 0.00 0.00 40.56 3.07
552 557 1.811266 CCGCACGAGGACTTCATGG 60.811 63.158 0.00 0.00 0.00 3.66
553 558 1.079819 CGCACGAGGACTTCATGGT 60.080 57.895 0.00 0.00 0.00 3.55
554 559 0.670546 CGCACGAGGACTTCATGGTT 60.671 55.000 0.00 0.00 0.00 3.67
555 560 1.403647 CGCACGAGGACTTCATGGTTA 60.404 52.381 0.00 0.00 0.00 2.85
556 561 2.738643 CGCACGAGGACTTCATGGTTAT 60.739 50.000 0.00 0.00 0.00 1.89
557 562 2.866762 GCACGAGGACTTCATGGTTATC 59.133 50.000 0.00 0.00 0.00 1.75
558 563 3.678806 GCACGAGGACTTCATGGTTATCA 60.679 47.826 0.00 0.00 0.00 2.15
559 564 4.697514 CACGAGGACTTCATGGTTATCAT 58.302 43.478 0.00 0.00 36.31 2.45
560 565 4.747108 CACGAGGACTTCATGGTTATCATC 59.253 45.833 0.00 0.00 32.92 2.92
561 566 4.405680 ACGAGGACTTCATGGTTATCATCA 59.594 41.667 0.00 0.00 32.92 3.07
562 567 4.987285 CGAGGACTTCATGGTTATCATCAG 59.013 45.833 0.00 0.00 32.92 2.90
563 568 4.712476 AGGACTTCATGGTTATCATCAGC 58.288 43.478 0.00 0.00 32.92 4.26
564 569 3.817647 GGACTTCATGGTTATCATCAGCC 59.182 47.826 0.00 0.00 32.92 4.85
565 570 3.470709 ACTTCATGGTTATCATCAGCCG 58.529 45.455 0.00 0.00 32.92 5.52
566 571 2.549064 TCATGGTTATCATCAGCCGG 57.451 50.000 0.00 0.00 32.92 6.13
567 572 1.768275 TCATGGTTATCATCAGCCGGT 59.232 47.619 1.90 0.00 32.92 5.28
568 573 2.969262 TCATGGTTATCATCAGCCGGTA 59.031 45.455 1.90 0.00 32.92 4.02
569 574 3.006859 TCATGGTTATCATCAGCCGGTAG 59.993 47.826 1.90 0.00 32.92 3.18
570 575 1.691976 TGGTTATCATCAGCCGGTAGG 59.308 52.381 1.90 0.00 41.62 3.18
571 576 1.002087 GGTTATCATCAGCCGGTAGGG 59.998 57.143 1.90 0.00 38.20 3.53
572 577 1.968493 GTTATCATCAGCCGGTAGGGA 59.032 52.381 1.90 0.00 38.47 4.20
573 578 1.629043 TATCATCAGCCGGTAGGGAC 58.371 55.000 1.90 0.00 38.47 4.46
574 579 0.105453 ATCATCAGCCGGTAGGGACT 60.105 55.000 1.90 0.00 46.37 3.85
575 580 1.043116 TCATCAGCCGGTAGGGACTG 61.043 60.000 1.90 0.00 41.52 3.51
576 581 2.435693 ATCAGCCGGTAGGGACTGC 61.436 63.158 1.90 0.00 41.52 4.40
577 582 3.390521 CAGCCGGTAGGGACTGCA 61.391 66.667 1.90 0.00 44.97 4.41
578 583 2.606519 AGCCGGTAGGGACTGCAA 60.607 61.111 1.90 0.00 44.97 4.08
579 584 2.436115 GCCGGTAGGGACTGCAAC 60.436 66.667 1.90 0.00 44.97 4.17
580 585 3.065306 CCGGTAGGGACTGCAACA 58.935 61.111 0.00 0.00 44.97 3.33
581 586 1.373435 CCGGTAGGGACTGCAACAA 59.627 57.895 0.00 0.00 44.97 2.83
582 587 0.250553 CCGGTAGGGACTGCAACAAA 60.251 55.000 0.00 0.00 44.97 2.83
583 588 1.600023 CGGTAGGGACTGCAACAAAA 58.400 50.000 0.00 0.00 44.97 2.44
584 589 2.159382 CGGTAGGGACTGCAACAAAAT 58.841 47.619 0.00 0.00 44.97 1.82
585 590 2.095263 CGGTAGGGACTGCAACAAAATG 60.095 50.000 0.00 0.00 44.97 2.32
586 591 2.890945 GGTAGGGACTGCAACAAAATGT 59.109 45.455 0.00 0.00 44.97 2.71
587 592 4.076394 GGTAGGGACTGCAACAAAATGTA 58.924 43.478 0.00 0.00 44.97 2.29
588 593 4.082949 GGTAGGGACTGCAACAAAATGTAC 60.083 45.833 0.00 0.00 44.97 2.90
589 594 2.552315 AGGGACTGCAACAAAATGTACG 59.448 45.455 0.00 0.00 37.18 3.67
590 595 2.292292 GGGACTGCAACAAAATGTACGT 59.708 45.455 0.00 0.00 0.00 3.57
591 596 3.499157 GGGACTGCAACAAAATGTACGTA 59.501 43.478 0.00 0.00 0.00 3.57
592 597 4.378046 GGGACTGCAACAAAATGTACGTAG 60.378 45.833 0.00 0.00 0.00 3.51
593 598 4.449743 GGACTGCAACAAAATGTACGTAGA 59.550 41.667 0.00 0.00 0.00 2.59
594 599 5.049954 GGACTGCAACAAAATGTACGTAGAA 60.050 40.000 0.00 0.00 0.00 2.10
595 600 6.348213 GGACTGCAACAAAATGTACGTAGAAT 60.348 38.462 0.00 0.00 0.00 2.40
596 601 7.148540 GGACTGCAACAAAATGTACGTAGAATA 60.149 37.037 0.00 0.00 0.00 1.75
597 602 7.739295 ACTGCAACAAAATGTACGTAGAATAG 58.261 34.615 0.00 0.00 0.00 1.73
598 603 7.067532 TGCAACAAAATGTACGTAGAATAGG 57.932 36.000 0.00 0.00 0.00 2.57
599 604 6.651643 TGCAACAAAATGTACGTAGAATAGGT 59.348 34.615 0.00 0.00 42.96 3.08
600 605 7.148540 TGCAACAAAATGTACGTAGAATAGGTC 60.149 37.037 0.00 0.00 40.57 3.85
601 606 7.064253 GCAACAAAATGTACGTAGAATAGGTCT 59.936 37.037 0.00 0.00 40.57 3.85
602 607 9.577110 CAACAAAATGTACGTAGAATAGGTCTA 57.423 33.333 0.00 0.00 40.57 2.59
738 743 1.202952 ACCCAAAATGCCGGTGACTAA 60.203 47.619 1.90 0.00 0.00 2.24
1247 1331 4.866508 TCTCTGTACAGTGTTAGGGTTG 57.133 45.455 21.99 0.00 0.00 3.77
1304 1389 6.561737 TTAATGAACCGTGCAAGTTGATTA 57.438 33.333 14.63 14.63 33.83 1.75
1307 1392 4.068599 TGAACCGTGCAAGTTGATTATGA 58.931 39.130 7.16 0.00 0.00 2.15
1323 1410 8.615211 GTTGATTATGATGTTGAGTGCAGATTA 58.385 33.333 0.00 0.00 0.00 1.75
1468 1555 0.102120 CGTGTTGCTTTTGAAGGGCA 59.898 50.000 0.00 0.00 0.00 5.36
1647 1754 9.515020 AAACTTAATCATGGCATTGTAATAACG 57.485 29.630 0.00 0.00 0.00 3.18
2076 2190 1.271597 CCAGAAACAAGTGGAGGAGGG 60.272 57.143 0.00 0.00 35.67 4.30
2259 2376 6.957020 AGAGATGTTCTTAAGAAGGAGAAGGA 59.043 38.462 18.22 0.00 34.27 3.36
2449 2566 6.252995 AGTGATTATGGGTGTACATTTTGGT 58.747 36.000 0.00 0.00 32.39 3.67
2705 2824 1.988015 GGCTTAGTGGCCCACTACA 59.012 57.895 23.13 13.08 45.13 2.74
2727 2846 2.749621 CTCTGACCAAATGCAACCCTAC 59.250 50.000 0.00 0.00 0.00 3.18
2728 2847 1.818674 CTGACCAAATGCAACCCTACC 59.181 52.381 0.00 0.00 0.00 3.18
2742 2862 2.115973 ACCCTACCCCTACTAAACCCAA 59.884 50.000 0.00 0.00 0.00 4.12
2743 2863 2.507058 CCCTACCCCTACTAAACCCAAC 59.493 54.545 0.00 0.00 0.00 3.77
2904 3026 2.967473 GACAGCAGCAGCAGCACAG 61.967 63.158 12.92 4.09 45.49 3.66
2905 3027 2.668550 CAGCAGCAGCAGCACAGA 60.669 61.111 12.92 0.00 45.49 3.41
2906 3028 2.358860 AGCAGCAGCAGCACAGAG 60.359 61.111 12.92 0.00 45.49 3.35
2961 3095 4.802051 GCGGCCCAGGATGAGCAA 62.802 66.667 0.00 0.00 39.69 3.91
3022 3156 5.258841 TGGAGAAGTGCAATGATGAAGAAT 58.741 37.500 0.00 0.00 0.00 2.40
3028 3162 8.045507 AGAAGTGCAATGATGAAGAATTAGAGA 58.954 33.333 0.00 0.00 0.00 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.912220 CGCCTTAACATGAGGGGGA 59.088 57.895 0.00 0.00 41.95 4.81
19 20 4.011023 GGAAGGAGAACTTTTTCCTAGCC 58.989 47.826 1.62 3.74 42.95 3.93
26 27 4.281941 GCTTGGATGGAAGGAGAACTTTTT 59.718 41.667 0.00 0.00 40.21 1.94
72 73 1.307691 AGCAAGCAGAGGGGAGGAT 60.308 57.895 0.00 0.00 0.00 3.24
124 125 1.888436 CTAGTCCAAGCCGAGGCACA 61.888 60.000 17.18 0.00 44.88 4.57
132 133 5.417754 AACCTAAACTACTAGTCCAAGCC 57.582 43.478 0.00 0.00 0.00 4.35
136 137 8.890410 AACATCTAACCTAAACTACTAGTCCA 57.110 34.615 0.00 0.00 0.00 4.02
178 179 1.007734 GTCACCTGTCGAAGCGTCA 60.008 57.895 0.00 0.00 0.00 4.35
195 196 0.960364 AATCAAAGATGGTGCGCCGT 60.960 50.000 11.77 11.77 37.67 5.68
224 225 2.183679 ACTCAGGGAGAATCGAAGCTT 58.816 47.619 0.00 0.00 34.37 3.74
232 233 1.938585 TGGACGAACTCAGGGAGAAT 58.061 50.000 0.00 0.00 33.32 2.40
240 241 5.462530 TTCTGTCTTAATGGACGAACTCA 57.537 39.130 0.00 0.00 38.91 3.41
245 246 5.789521 TGTTGATTCTGTCTTAATGGACGA 58.210 37.500 0.00 0.00 38.91 4.20
251 252 5.353678 GCAGCTCTGTTGATTCTGTCTTAAT 59.646 40.000 0.00 0.00 0.00 1.40
253 254 4.248859 GCAGCTCTGTTGATTCTGTCTTA 58.751 43.478 0.00 0.00 0.00 2.10
292 293 0.978146 CCTCGTCACCCCAAGGAGAT 60.978 60.000 0.00 0.00 35.03 2.75
325 326 3.498834 GCCATCACGCACGCATGA 61.499 61.111 0.00 0.00 0.00 3.07
361 366 5.289595 TCGAACCCTTGAATCGATATGAAG 58.710 41.667 0.00 1.21 40.34 3.02
379 384 1.267932 CCGTAGTCGTCATCCTCGAAC 60.268 57.143 0.00 0.00 39.01 3.95
380 385 1.012086 CCGTAGTCGTCATCCTCGAA 58.988 55.000 0.00 0.00 39.01 3.71
381 386 1.434622 GCCGTAGTCGTCATCCTCGA 61.435 60.000 0.00 0.00 35.01 4.04
382 387 1.009900 GCCGTAGTCGTCATCCTCG 60.010 63.158 0.00 0.00 35.01 4.63
383 388 0.308376 GAGCCGTAGTCGTCATCCTC 59.692 60.000 0.00 0.00 35.01 3.71
384 389 1.102222 GGAGCCGTAGTCGTCATCCT 61.102 60.000 0.00 0.00 35.01 3.24
385 390 1.359475 GGAGCCGTAGTCGTCATCC 59.641 63.158 0.00 0.00 35.01 3.51
386 391 0.029567 CTGGAGCCGTAGTCGTCATC 59.970 60.000 0.00 0.00 35.01 2.92
387 392 0.393944 TCTGGAGCCGTAGTCGTCAT 60.394 55.000 0.00 0.00 35.01 3.06
388 393 1.002990 TCTGGAGCCGTAGTCGTCA 60.003 57.895 0.00 0.00 35.01 4.35
389 394 1.025647 AGTCTGGAGCCGTAGTCGTC 61.026 60.000 0.00 0.00 35.01 4.20
390 395 1.002379 AGTCTGGAGCCGTAGTCGT 60.002 57.895 0.00 0.00 35.01 4.34
391 396 1.429825 CAGTCTGGAGCCGTAGTCG 59.570 63.158 0.00 0.00 0.00 4.18
392 397 1.139947 GCAGTCTGGAGCCGTAGTC 59.860 63.158 1.14 0.00 0.00 2.59
393 398 1.304547 AGCAGTCTGGAGCCGTAGT 60.305 57.895 1.14 0.00 0.00 2.73
394 399 1.140589 CAGCAGTCTGGAGCCGTAG 59.859 63.158 1.14 0.00 36.68 3.51
395 400 3.288484 CAGCAGTCTGGAGCCGTA 58.712 61.111 1.14 0.00 36.68 4.02
403 408 0.539051 CCCTAAGGACCAGCAGTCTG 59.461 60.000 6.83 0.00 45.54 3.51
404 409 0.618968 CCCCTAAGGACCAGCAGTCT 60.619 60.000 6.83 0.00 45.54 3.24
405 410 1.908483 CCCCTAAGGACCAGCAGTC 59.092 63.158 0.00 0.00 45.51 3.51
406 411 2.301738 GCCCCTAAGGACCAGCAGT 61.302 63.158 0.00 0.00 38.24 4.40
407 412 2.592308 GCCCCTAAGGACCAGCAG 59.408 66.667 0.00 0.00 38.24 4.24
408 413 3.399181 CGCCCCTAAGGACCAGCA 61.399 66.667 0.00 0.00 38.24 4.41
409 414 4.858680 GCGCCCCTAAGGACCAGC 62.859 72.222 0.00 0.00 38.24 4.85
410 415 4.530857 CGCGCCCCTAAGGACCAG 62.531 72.222 0.00 0.00 38.24 4.00
412 417 4.832608 CACGCGCCCCTAAGGACC 62.833 72.222 5.73 0.00 38.24 4.46
415 420 4.856801 ATGCACGCGCCCCTAAGG 62.857 66.667 5.73 0.00 37.32 2.69
416 421 3.576356 CATGCACGCGCCCCTAAG 61.576 66.667 5.73 0.00 37.32 2.18
417 422 4.089239 TCATGCACGCGCCCCTAA 62.089 61.111 5.73 0.00 37.32 2.69
418 423 4.529219 CTCATGCACGCGCCCCTA 62.529 66.667 5.73 0.00 37.32 3.53
423 428 3.088500 GAAGTCCTCATGCACGCGC 62.089 63.158 5.73 0.00 39.24 6.86
424 429 1.086067 ATGAAGTCCTCATGCACGCG 61.086 55.000 3.53 3.53 43.49 6.01
425 430 2.772739 ATGAAGTCCTCATGCACGC 58.227 52.632 0.00 0.00 43.49 5.34
431 436 6.505048 TGATGATAACCATGAAGTCCTCAT 57.495 37.500 0.00 0.00 46.25 2.90
432 437 5.685861 GCTGATGATAACCATGAAGTCCTCA 60.686 44.000 0.00 0.00 38.81 3.86
433 438 4.754114 GCTGATGATAACCATGAAGTCCTC 59.246 45.833 0.00 0.00 35.17 3.71
434 439 4.164796 TGCTGATGATAACCATGAAGTCCT 59.835 41.667 0.00 0.00 35.17 3.85
435 440 4.454678 TGCTGATGATAACCATGAAGTCC 58.545 43.478 0.00 0.00 35.17 3.85
436 441 5.008415 CCTTGCTGATGATAACCATGAAGTC 59.992 44.000 0.00 0.00 35.17 3.01
437 442 4.885907 CCTTGCTGATGATAACCATGAAGT 59.114 41.667 0.00 0.00 35.17 3.01
438 443 4.885907 ACCTTGCTGATGATAACCATGAAG 59.114 41.667 0.00 0.00 35.17 3.02
439 444 4.858850 ACCTTGCTGATGATAACCATGAA 58.141 39.130 0.00 0.00 35.17 2.57
440 445 4.508551 ACCTTGCTGATGATAACCATGA 57.491 40.909 0.00 0.00 35.17 3.07
441 446 5.240183 CCTAACCTTGCTGATGATAACCATG 59.760 44.000 0.00 0.00 35.17 3.66
442 447 5.103940 ACCTAACCTTGCTGATGATAACCAT 60.104 40.000 0.00 0.00 38.43 3.55
443 448 4.227300 ACCTAACCTTGCTGATGATAACCA 59.773 41.667 0.00 0.00 0.00 3.67
444 449 4.781934 ACCTAACCTTGCTGATGATAACC 58.218 43.478 0.00 0.00 0.00 2.85
445 450 4.508124 CGACCTAACCTTGCTGATGATAAC 59.492 45.833 0.00 0.00 0.00 1.89
446 451 4.442893 CCGACCTAACCTTGCTGATGATAA 60.443 45.833 0.00 0.00 0.00 1.75
447 452 3.069586 CCGACCTAACCTTGCTGATGATA 59.930 47.826 0.00 0.00 0.00 2.15
448 453 2.158900 CCGACCTAACCTTGCTGATGAT 60.159 50.000 0.00 0.00 0.00 2.45
449 454 1.207089 CCGACCTAACCTTGCTGATGA 59.793 52.381 0.00 0.00 0.00 2.92
450 455 1.656652 CCGACCTAACCTTGCTGATG 58.343 55.000 0.00 0.00 0.00 3.07
451 456 0.107654 GCCGACCTAACCTTGCTGAT 60.108 55.000 0.00 0.00 0.00 2.90
452 457 1.192146 AGCCGACCTAACCTTGCTGA 61.192 55.000 0.00 0.00 0.00 4.26
453 458 0.741221 GAGCCGACCTAACCTTGCTG 60.741 60.000 0.00 0.00 0.00 4.41
454 459 1.597461 GAGCCGACCTAACCTTGCT 59.403 57.895 0.00 0.00 0.00 3.91
455 460 1.449778 GGAGCCGACCTAACCTTGC 60.450 63.158 0.00 0.00 0.00 4.01
456 461 0.108138 CTGGAGCCGACCTAACCTTG 60.108 60.000 0.00 0.00 0.00 3.61
457 462 0.544595 ACTGGAGCCGACCTAACCTT 60.545 55.000 0.00 0.00 0.00 3.50
458 463 0.333993 TACTGGAGCCGACCTAACCT 59.666 55.000 0.00 0.00 0.00 3.50
459 464 1.068741 CATACTGGAGCCGACCTAACC 59.931 57.143 0.00 0.00 0.00 2.85
460 465 2.029623 TCATACTGGAGCCGACCTAAC 58.970 52.381 0.00 0.00 0.00 2.34
461 466 2.447408 TCATACTGGAGCCGACCTAA 57.553 50.000 0.00 0.00 0.00 2.69
462 467 2.447408 TTCATACTGGAGCCGACCTA 57.553 50.000 0.00 0.00 0.00 3.08
463 468 1.568504 TTTCATACTGGAGCCGACCT 58.431 50.000 0.00 0.00 0.00 3.85
464 469 2.007608 GTTTTCATACTGGAGCCGACC 58.992 52.381 0.00 0.00 0.00 4.79
465 470 1.659098 CGTTTTCATACTGGAGCCGAC 59.341 52.381 0.00 0.00 0.00 4.79
466 471 1.404986 CCGTTTTCATACTGGAGCCGA 60.405 52.381 0.00 0.00 0.00 5.54
467 472 1.006832 CCGTTTTCATACTGGAGCCG 58.993 55.000 0.00 0.00 0.00 5.52
468 473 0.733150 GCCGTTTTCATACTGGAGCC 59.267 55.000 0.00 0.00 0.00 4.70
469 474 0.373716 CGCCGTTTTCATACTGGAGC 59.626 55.000 0.00 0.00 0.00 4.70
470 475 1.659098 GTCGCCGTTTTCATACTGGAG 59.341 52.381 0.00 0.00 0.00 3.86
471 476 1.001068 TGTCGCCGTTTTCATACTGGA 59.999 47.619 0.00 0.00 0.00 3.86
472 477 1.434555 TGTCGCCGTTTTCATACTGG 58.565 50.000 0.00 0.00 0.00 4.00
473 478 2.222213 TGTTGTCGCCGTTTTCATACTG 59.778 45.455 0.00 0.00 0.00 2.74
474 479 2.485903 TGTTGTCGCCGTTTTCATACT 58.514 42.857 0.00 0.00 0.00 2.12
475 480 2.953640 TGTTGTCGCCGTTTTCATAC 57.046 45.000 0.00 0.00 0.00 2.39
476 481 2.612672 TGTTGTTGTCGCCGTTTTCATA 59.387 40.909 0.00 0.00 0.00 2.15
477 482 1.402259 TGTTGTTGTCGCCGTTTTCAT 59.598 42.857 0.00 0.00 0.00 2.57
478 483 0.803117 TGTTGTTGTCGCCGTTTTCA 59.197 45.000 0.00 0.00 0.00 2.69
479 484 1.185189 GTGTTGTTGTCGCCGTTTTC 58.815 50.000 0.00 0.00 0.00 2.29
480 485 0.806241 AGTGTTGTTGTCGCCGTTTT 59.194 45.000 0.00 0.00 0.00 2.43
481 486 0.375803 GAGTGTTGTTGTCGCCGTTT 59.624 50.000 0.00 0.00 0.00 3.60
482 487 0.461339 AGAGTGTTGTTGTCGCCGTT 60.461 50.000 0.00 0.00 0.00 4.44
483 488 0.386476 TAGAGTGTTGTTGTCGCCGT 59.614 50.000 0.00 0.00 0.00 5.68
484 489 1.654105 GATAGAGTGTTGTTGTCGCCG 59.346 52.381 0.00 0.00 0.00 6.46
485 490 2.000447 GGATAGAGTGTTGTTGTCGCC 59.000 52.381 0.00 0.00 0.00 5.54
486 491 1.654105 CGGATAGAGTGTTGTTGTCGC 59.346 52.381 0.00 0.00 0.00 5.19
487 492 1.654105 GCGGATAGAGTGTTGTTGTCG 59.346 52.381 0.00 0.00 0.00 4.35
488 493 2.960819 AGCGGATAGAGTGTTGTTGTC 58.039 47.619 0.00 0.00 0.00 3.18
489 494 3.510360 ACTAGCGGATAGAGTGTTGTTGT 59.490 43.478 7.37 0.00 35.30 3.32
490 495 4.111375 ACTAGCGGATAGAGTGTTGTTG 57.889 45.455 7.37 0.00 35.30 3.33
491 496 4.803098 AACTAGCGGATAGAGTGTTGTT 57.197 40.909 7.37 0.00 35.30 2.83
492 497 4.803098 AAACTAGCGGATAGAGTGTTGT 57.197 40.909 7.37 0.00 35.30 3.32
493 498 4.201724 GCAAAACTAGCGGATAGAGTGTTG 60.202 45.833 7.37 1.15 40.13 3.33
494 499 3.933332 GCAAAACTAGCGGATAGAGTGTT 59.067 43.478 7.37 0.00 35.30 3.32
495 500 3.522553 GCAAAACTAGCGGATAGAGTGT 58.477 45.455 7.37 0.00 35.30 3.55
496 501 2.866762 GGCAAAACTAGCGGATAGAGTG 59.133 50.000 7.37 3.23 35.30 3.51
497 502 2.481449 CGGCAAAACTAGCGGATAGAGT 60.481 50.000 7.37 0.00 35.30 3.24
498 503 2.128035 CGGCAAAACTAGCGGATAGAG 58.872 52.381 7.37 0.00 35.30 2.43
499 504 1.202486 CCGGCAAAACTAGCGGATAGA 60.202 52.381 7.37 0.00 35.30 1.98
500 505 1.217882 CCGGCAAAACTAGCGGATAG 58.782 55.000 0.00 0.00 37.53 2.08
501 506 0.812412 GCCGGCAAAACTAGCGGATA 60.812 55.000 24.80 0.00 34.65 2.59
502 507 2.112815 GCCGGCAAAACTAGCGGAT 61.113 57.895 24.80 0.00 34.65 4.18
503 508 2.744709 GCCGGCAAAACTAGCGGA 60.745 61.111 24.80 0.00 34.65 5.54
504 509 4.160635 CGCCGGCAAAACTAGCGG 62.161 66.667 28.98 0.98 42.93 5.52
505 510 4.160635 CCGCCGGCAAAACTAGCG 62.161 66.667 28.98 8.70 46.04 4.26
506 511 1.702491 CTACCGCCGGCAAAACTAGC 61.702 60.000 28.98 0.00 0.00 3.42
507 512 0.390735 ACTACCGCCGGCAAAACTAG 60.391 55.000 28.98 17.48 0.00 2.57
508 513 0.671163 CACTACCGCCGGCAAAACTA 60.671 55.000 28.98 6.31 0.00 2.24
509 514 1.964373 CACTACCGCCGGCAAAACT 60.964 57.895 28.98 5.35 0.00 2.66
510 515 1.303091 ATCACTACCGCCGGCAAAAC 61.303 55.000 28.98 0.00 0.00 2.43
511 516 0.606944 AATCACTACCGCCGGCAAAA 60.607 50.000 28.98 9.50 0.00 2.44
512 517 1.003112 AATCACTACCGCCGGCAAA 60.003 52.632 28.98 9.91 0.00 3.68
513 518 1.743623 CAATCACTACCGCCGGCAA 60.744 57.895 28.98 10.32 0.00 4.52
514 519 2.125310 CAATCACTACCGCCGGCA 60.125 61.111 28.98 5.90 0.00 5.69
515 520 1.702491 GAACAATCACTACCGCCGGC 61.702 60.000 19.07 19.07 0.00 6.13
516 521 1.087771 GGAACAATCACTACCGCCGG 61.088 60.000 0.00 0.00 0.00 6.13
517 522 1.418342 CGGAACAATCACTACCGCCG 61.418 60.000 0.00 0.00 37.32 6.46
518 523 2.380081 CGGAACAATCACTACCGCC 58.620 57.895 0.00 0.00 37.32 6.13
520 525 0.719465 GTGCGGAACAATCACTACCG 59.281 55.000 0.00 0.00 45.26 4.02
521 526 0.719465 CGTGCGGAACAATCACTACC 59.281 55.000 0.00 0.00 0.00 3.18
522 527 1.654105 CTCGTGCGGAACAATCACTAC 59.346 52.381 0.00 0.00 0.00 2.73
523 528 1.403647 CCTCGTGCGGAACAATCACTA 60.404 52.381 0.00 0.00 0.00 2.74
524 529 0.670546 CCTCGTGCGGAACAATCACT 60.671 55.000 0.00 0.00 0.00 3.41
525 530 0.669318 TCCTCGTGCGGAACAATCAC 60.669 55.000 0.00 0.00 0.00 3.06
526 531 0.669318 GTCCTCGTGCGGAACAATCA 60.669 55.000 0.00 0.00 34.20 2.57
527 532 0.389948 AGTCCTCGTGCGGAACAATC 60.390 55.000 0.00 0.00 34.20 2.67
528 533 0.034896 AAGTCCTCGTGCGGAACAAT 59.965 50.000 0.00 0.00 34.20 2.71
529 534 0.599204 GAAGTCCTCGTGCGGAACAA 60.599 55.000 0.00 0.00 34.20 2.83
530 535 1.006571 GAAGTCCTCGTGCGGAACA 60.007 57.895 0.00 0.00 34.20 3.18
531 536 0.389948 ATGAAGTCCTCGTGCGGAAC 60.390 55.000 0.00 0.00 34.20 3.62
532 537 0.389817 CATGAAGTCCTCGTGCGGAA 60.390 55.000 0.00 0.00 34.31 4.30
533 538 1.215382 CATGAAGTCCTCGTGCGGA 59.785 57.895 0.00 0.00 34.31 5.54
534 539 1.811266 CCATGAAGTCCTCGTGCGG 60.811 63.158 0.00 0.00 39.43 5.69
535 540 0.670546 AACCATGAAGTCCTCGTGCG 60.671 55.000 0.00 0.00 39.43 5.34
536 541 2.380084 TAACCATGAAGTCCTCGTGC 57.620 50.000 0.00 0.00 39.43 5.34
537 542 4.123497 TGATAACCATGAAGTCCTCGTG 57.877 45.455 0.00 0.00 40.32 4.35
538 543 4.405680 TGATGATAACCATGAAGTCCTCGT 59.594 41.667 0.00 0.00 35.17 4.18
539 544 4.948847 TGATGATAACCATGAAGTCCTCG 58.051 43.478 0.00 0.00 35.17 4.63
540 545 4.754114 GCTGATGATAACCATGAAGTCCTC 59.246 45.833 0.00 0.00 35.17 3.71
541 546 4.445448 GGCTGATGATAACCATGAAGTCCT 60.445 45.833 0.00 0.00 35.17 3.85
542 547 3.817647 GGCTGATGATAACCATGAAGTCC 59.182 47.826 0.00 0.00 35.17 3.85
543 548 3.496130 CGGCTGATGATAACCATGAAGTC 59.504 47.826 0.00 0.00 35.17 3.01
544 549 3.470709 CGGCTGATGATAACCATGAAGT 58.529 45.455 0.00 0.00 35.17 3.01
545 550 2.810274 CCGGCTGATGATAACCATGAAG 59.190 50.000 0.00 0.00 35.17 3.02
546 551 2.172505 ACCGGCTGATGATAACCATGAA 59.827 45.455 0.00 0.00 35.17 2.57
547 552 1.768275 ACCGGCTGATGATAACCATGA 59.232 47.619 0.00 0.00 35.17 3.07
548 553 2.260844 ACCGGCTGATGATAACCATG 57.739 50.000 0.00 0.00 35.17 3.66
549 554 2.303022 CCTACCGGCTGATGATAACCAT 59.697 50.000 0.00 0.00 38.43 3.55
550 555 1.691976 CCTACCGGCTGATGATAACCA 59.308 52.381 0.00 0.00 0.00 3.67
551 556 1.002087 CCCTACCGGCTGATGATAACC 59.998 57.143 0.00 0.00 0.00 2.85
552 557 1.968493 TCCCTACCGGCTGATGATAAC 59.032 52.381 0.00 0.00 0.00 1.89
553 558 1.968493 GTCCCTACCGGCTGATGATAA 59.032 52.381 0.00 0.00 0.00 1.75
554 559 1.147191 AGTCCCTACCGGCTGATGATA 59.853 52.381 0.00 0.00 0.00 2.15
555 560 0.105453 AGTCCCTACCGGCTGATGAT 60.105 55.000 0.00 0.00 0.00 2.45
556 561 1.043116 CAGTCCCTACCGGCTGATGA 61.043 60.000 0.00 0.00 37.75 2.92
557 562 1.443407 CAGTCCCTACCGGCTGATG 59.557 63.158 0.00 0.00 37.75 3.07
558 563 2.435693 GCAGTCCCTACCGGCTGAT 61.436 63.158 0.00 0.00 37.75 2.90
559 564 3.075005 GCAGTCCCTACCGGCTGA 61.075 66.667 0.00 0.00 37.75 4.26
560 565 2.954684 TTGCAGTCCCTACCGGCTG 61.955 63.158 0.00 0.00 38.25 4.85
561 566 2.606519 TTGCAGTCCCTACCGGCT 60.607 61.111 0.00 0.00 0.00 5.52
562 567 2.436115 GTTGCAGTCCCTACCGGC 60.436 66.667 0.00 0.00 0.00 6.13
563 568 0.250553 TTTGTTGCAGTCCCTACCGG 60.251 55.000 0.00 0.00 0.00 5.28
564 569 1.600023 TTTTGTTGCAGTCCCTACCG 58.400 50.000 0.00 0.00 0.00 4.02
565 570 2.890945 ACATTTTGTTGCAGTCCCTACC 59.109 45.455 0.00 0.00 0.00 3.18
566 571 4.378046 CGTACATTTTGTTGCAGTCCCTAC 60.378 45.833 0.00 0.00 0.00 3.18
567 572 3.749088 CGTACATTTTGTTGCAGTCCCTA 59.251 43.478 0.00 0.00 0.00 3.53
568 573 2.552315 CGTACATTTTGTTGCAGTCCCT 59.448 45.455 0.00 0.00 0.00 4.20
569 574 2.292292 ACGTACATTTTGTTGCAGTCCC 59.708 45.455 0.00 0.00 0.00 4.46
570 575 3.619233 ACGTACATTTTGTTGCAGTCC 57.381 42.857 0.00 0.00 0.00 3.85
571 576 5.585500 TCTACGTACATTTTGTTGCAGTC 57.415 39.130 0.00 0.00 0.00 3.51
572 577 5.994887 TTCTACGTACATTTTGTTGCAGT 57.005 34.783 0.00 0.00 0.00 4.40
573 578 7.148474 ACCTATTCTACGTACATTTTGTTGCAG 60.148 37.037 0.00 0.00 0.00 4.41
574 579 6.651643 ACCTATTCTACGTACATTTTGTTGCA 59.348 34.615 0.00 0.00 0.00 4.08
575 580 7.064253 AGACCTATTCTACGTACATTTTGTTGC 59.936 37.037 0.00 0.00 30.17 4.17
576 581 8.475331 AGACCTATTCTACGTACATTTTGTTG 57.525 34.615 0.00 0.00 30.17 3.33
584 589 9.903682 GCATTTTATAGACCTATTCTACGTACA 57.096 33.333 0.00 0.00 39.78 2.90
585 590 9.059485 CGCATTTTATAGACCTATTCTACGTAC 57.941 37.037 0.00 0.00 39.78 3.67
586 591 9.002600 TCGCATTTTATAGACCTATTCTACGTA 57.997 33.333 0.00 0.00 39.78 3.57
587 592 7.879070 TCGCATTTTATAGACCTATTCTACGT 58.121 34.615 0.00 0.00 39.78 3.57
588 593 8.021973 ACTCGCATTTTATAGACCTATTCTACG 58.978 37.037 0.00 0.00 39.78 3.51
595 600 9.635520 GCTATTTACTCGCATTTTATAGACCTA 57.364 33.333 0.00 0.00 0.00 3.08
596 601 8.148351 TGCTATTTACTCGCATTTTATAGACCT 58.852 33.333 0.00 0.00 0.00 3.85
597 602 8.306680 TGCTATTTACTCGCATTTTATAGACC 57.693 34.615 0.00 0.00 0.00 3.85
605 610 9.931210 GTAGTTTTATGCTATTTACTCGCATTT 57.069 29.630 1.07 0.00 41.22 2.32
606 611 9.326413 AGTAGTTTTATGCTATTTACTCGCATT 57.674 29.630 1.07 0.00 41.22 3.56
607 612 8.888579 AGTAGTTTTATGCTATTTACTCGCAT 57.111 30.769 0.00 0.00 45.45 4.73
608 613 9.459640 CTAGTAGTTTTATGCTATTTACTCGCA 57.540 33.333 0.00 0.00 38.14 5.10
673 678 5.238583 CGACTGGTAGGTTTCTGAGAAAAT 58.761 41.667 9.51 4.30 0.00 1.82
686 691 4.430765 AACCGCGCGACTGGTAGG 62.431 66.667 34.63 14.59 37.54 3.18
726 731 0.604073 TCAATCGTTAGTCACCGGCA 59.396 50.000 0.00 0.00 0.00 5.69
738 743 3.002965 GGTCAGAAAAACGGTTCAATCGT 59.997 43.478 0.00 0.00 43.14 3.73
809 814 1.666872 GCTAACGGCTGTCAACGGT 60.667 57.895 0.00 0.00 38.06 4.83
1304 1389 7.458409 AGTTTTAATCTGCACTCAACATCAT 57.542 32.000 0.00 0.00 0.00 2.45
1307 1392 7.445402 ACACTAGTTTTAATCTGCACTCAACAT 59.555 33.333 0.00 0.00 0.00 2.71
1323 1410 7.494298 CCAAAATAACCAGCAAACACTAGTTTT 59.506 33.333 0.00 0.00 45.32 2.43
1468 1555 5.357032 CCATAGAAACGCCTTCCTGTTAAAT 59.643 40.000 0.00 0.00 34.21 1.40
1752 1863 8.034215 TCACACCATTTTCCTGCATTTATAAAG 58.966 33.333 3.94 0.00 0.00 1.85
1880 1994 7.009179 TCTCAAACTTCTCCTTGTCATGTAT 57.991 36.000 0.00 0.00 0.00 2.29
2076 2190 6.754193 TCCTTCTTCTTCTTCTCAAGTTCTC 58.246 40.000 0.00 0.00 0.00 2.87
2449 2566 6.597562 ACACTAGGTTAAACTTCACATTCCA 58.402 36.000 0.00 0.00 0.00 3.53
2705 2824 1.145738 AGGGTTGCATTTGGTCAGAGT 59.854 47.619 0.00 0.00 0.00 3.24
2727 2846 0.627451 GGGGTTGGGTTTAGTAGGGG 59.373 60.000 0.00 0.00 0.00 4.79
2728 2847 0.627451 GGGGGTTGGGTTTAGTAGGG 59.373 60.000 0.00 0.00 0.00 3.53
2742 2862 2.219216 ATTGAGAGATGGATGGGGGT 57.781 50.000 0.00 0.00 0.00 4.95
2743 2863 6.183347 GTTTATATTGAGAGATGGATGGGGG 58.817 44.000 0.00 0.00 0.00 5.40
2904 3026 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
2905 3027 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
2906 3028 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
2961 3095 0.250338 GGCGGTTGAACTCCTCTTGT 60.250 55.000 0.00 0.00 0.00 3.16
3022 3156 3.334691 CGCCAGTGAAAACCATCTCTAA 58.665 45.455 0.00 0.00 0.00 2.10
3028 3162 1.526575 CTGCCGCCAGTGAAAACCAT 61.527 55.000 0.00 0.00 34.31 3.55
3141 3285 5.705609 TTGACATATCAGTCATAGCGCTA 57.294 39.130 21.30 21.30 46.90 4.26


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.